How do you merge 2 areas of a single mesh into one?
I think you are watching sebastian lague's video. 

Now that you have created arms and the body, you want to join them. First, I must tell you that ctrl+J only makes joins meaning it doesn't join the faces or vertices but it makes both the mesh to be accessible by one name. 
Now for joining the hands with the body you need to follow these steps:-


You need to select two vertices one of the hand and other vertice of
the body nearest to the vertice selected before.
Press  alt + m while selecting the vertices. Select 'to center' and
now your the vertices are joined.
Repeat this step for all vertices.


The other way :-


Select your hand by hovering over it and press 'l'. Now you have
your hand selected.
Press P to separate the hand. This is the opposite of Ctrl + J.
Exit Edit mode.
Select your hand mesh and enter edit mode to extend the edges near
the top say shoulder.
Extend them by pressing E. So that the extended part touches the
body. Try to make the extended part as small as possible.
Now Exit Edit mode.
Go to modifiers tab and select boolean.
Select Union in boolean and then select your body mesh. Click Apply.
Now you have both the mesh joined. You can delete your body mesh
now.


I would recommend to follow the first way.

Hope this helps.